cuffdiff long noncoding annotation vs full annotation

Question

[nand]

I'm studying differential expression of long non coding RNA. Should I run cuffdiff using the gencode annotation file with all transcripts, and then filter out lncRNA data, or run cuffdiff with annotation of only long noncoding RNAs? If I use full transcripts annotation, FPKM values are much lower than that with only lncRNA transcripts. I prefer to use lncRNA annotation because it gives about ten times more significant transcripts.

Answer 1

[Ben]

You should align the clean reads to reference genome with the lncRNA gtf, then you can run cuffdiff using the lncRNA gtf